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extract_goodreader.py
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extract_goodreader.py
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#!/usr/bin/env python3
"""Process GoodReader email export into format accepted by `extract_dictation.py`."""
__author__ = "Joseph Reagle"
__copyright__ = "Copyright (C) 2009-2023 Joseph Reagle"
__license__ = "GLPv3"
__version__ = "1.0"
import argparse # http://docs.python.org/dev/library/argparse.html
import logging as log
import re
import subprocess
import sys
from email import policy
from email.parser import BytesParser
from pathlib import Path # https://docs.python.org/3/library/pathlib.html
import roman # type:ignore
from enchant import Dict # type:ignore # sometimes mismatch with system version
# https://pypi.org/project/pyenchant/
from enchant.checker import SpellChecker # type:ignore
from send2trash import send2trash # type:ignore
from extract_dictation import create_mm
from utils.extract import get_bib_preamble
from utils.text import smart_to_markdown
RE_ANNOTATION = re.compile(r"^(?P<kind>\w+) \((?P<color>\w+)\),")
RE_DOI = re.compile(r"10\.\d{4,9}/[-._;()/:A-Z0-9]+", re.IGNORECASE)
RE_FIRST = re.compile(r"^First = (\d+)", re.IGNORECASE | re.MULTILINE)
RE_ISBN = re.compile(r"978(?:-?\d){10}")
RE_JOIN_LINES = re.compile(r"([a-z] ?)\n\n([a-z])")
RE_PAGE_NUM = re.compile(
r"""---[ ]Page[ ]
(?:p\.[ ])?
\[?
(\d+|[A-Z]+|[ivxlc]+)
\]?
[ ]---""",
re.VERBOSE,
)
def process_text(args: argparse.Namespace, text: str) -> str:
"""Process text for annotation kind, color, and page number, joining lines as needed."""
"""
| first_specified | first_parsed | offset | parsed | result |
|-----------------|--------------|--------|--------|--------|
| 5 | 5 | 0 | 10 | 10 |
| 5 | 7 | -2 | 10 | 08 |
| 5 | 4 | 1 | 10 | 11 |
| -3 | 1 | -4 | 10 | 6 |
| 0 | 1 | None | 10 | 10 |
Table: exemplar values for page calculation
"""
# 1st page number specified in PDF comment
page_num_first_specfied: int = args.first # 1st page specified in args
page_num_first_parsed: int = 0 # 1st page number as parsed
page_num_offset: int = 0 # page number offset
page_num_parsed: int | str = 0 # page number parsed, can be roman
page_num_result: int | str = 0 # page number result, can be roman or ""
color = kind = prefix = ""
ignore_next_line = False
is_roman = False
text_joined = RE_JOIN_LINES.sub(r"\1\2", text) # remove spurious \n
if match := _get_group_n(RE_FIRST, text_joined, 1):
page_num_first_specfied = int(match)
log.debug(f"{page_num_first_specfied=}")
text_new = add_doi_isbn_info(text_joined)
for line in text_joined.split("\n"):
log.debug(f"setting {is_roman=}")
if line == "(report generated by GoodReader)": # end of notes
break
log.debug(f"******************** {line=}")
if not line.strip() or ignore_next_line:
ignore_next_line = False
continue
if line.startswith("Bookmark:"):
ignore_next_line = True
continue
if page_num_match := RE_PAGE_NUM.match(line):
log.info(f"{page_num_match=}")
page_num_parsed = str(page_num_match.group(1))
if page_num_parsed.isdigit():
page_num_parsed = int(page_num_parsed)
is_roman = False
elif page_num_parsed.isalpha():
if page_num_parsed.isupper():
page_num_parsed = ord(page_num_parsed) - 96
is_roman = False
# TODO: weird PDFs using uppercase, what's after "Z"?
else:
page_num_parsed = roman.fromRoman(page_num_parsed.upper())
is_roman = True
log.debug(f"setting {is_roman=}")
else:
print(f"unknown {page_num_parsed}")
sys.exit()
log.debug(f"{page_num_parsed=} SET")
if not page_num_first_parsed:
log.debug("SETTING initials")
page_num_first_parsed = int(page_num_parsed)
log.debug(f"{page_num_first_parsed=}")
if page_num_first_specfied:
page_num_offset = page_num_first_specfied - page_num_first_parsed
else:
page_num_offset = 0
log.debug(f"{page_num_offset=}")
elif annotation_match := RE_ANNOTATION.match(line):
log.debug("RE_ANNOTATION match")
log.debug(f"{page_num_parsed=}")
log.debug(f"{page_num_offset=}")
page_num_result = int(page_num_parsed) + page_num_offset
log.debug(f"{page_num_result=}")
# Kinds are either:
# - "Highlight (cyan)": section title
# - "Highlight (yellow)": excerpted text
# - "Note (yellow)": reader comment
kind, color = annotation_match.groupdict().values()
if kind == "Note":
prefix = "--"
page_num_result = ""
elif kind == "Highlight":
if color == "yellow":
prefix = "excerpt."
if color == "cyan":
prefix = "section."
page_num_result = ""
else:
log.debug(f"testing {is_roman=}")
if page_num_result and is_roman:
page_num_result = roman.toRoman(page_num_result).lower()
fixed_line = smart_to_markdown(clean_pdf_ocr(line))
log.debug(f"{page_num_result} {prefix} {fixed_line}".strip())
text_new.append(f"{page_num_result} {prefix} {fixed_line}".strip())
return "\n".join(text_new)
def add_doi_isbn_info(text_joined: str) -> list[str]:
"""If ISBN/DOI, add metadata."""
if DOI := _get_group_n(RE_DOI, text_joined, 0):
log.info(f"{DOI=}")
text_new = get_bib_preamble(DOI)
elif ISBN := _get_group_n(RE_ISBN, text_joined, 0):
log.info(f"{ISBN=}")
text_new = get_bib_preamble(ISBN)
else:
log.info("NO DOI or ISBN")
text_new = []
return text_new
def clean_pdf_ocr(text: str) -> str:
"""Remove OCR artifacts of junk hyphens and missing spaces."""
new_text = remove_junk_hyphens(text)
new_text = restore_lost_spaces(new_text)
return new_text
# This dependency on pyenchant tends to cause problems, but I need suggestion
def remove_junk_hyphens(
text: str,
hyphen_RE: re.Pattern = re.compile(r"([a-zA-Z]{2,})(-)([a-zA-Z]{2,})"),
enchant_d: Dict = Dict("en_US"), # noqa: B008 (performed once at definition)
) -> str:
"""Remove junk hyphens from PDFs using pyenchant.
Test if the constituent parts of hyphenated text are actual words.
>>> remove_junk_hyphens('Do out-calls for your co-worker until lu-nch-bre-ak.')
'Do out-calls for your co-worker until lunch-break.'
"""
matches = hyphen_RE.findall(text)
for match in matches:
hyphenated_word = match[0] + match[1] + match[2]
log.debug(f"{hyphenated_word=}")
log.debug(f"{enchant_d.check(match[0])=}")
log.debug(f"{enchant_d.check(match[2])=}")
if not (enchant_d.check(match[0]) and enchant_d.check(match[2])):
replacement = match[0] + match[2]
text = text.replace(hyphenated_word, replacement)
return text
# This dependency on pyenchant tends to cause problems, but I need suggestion
def restore_lost_spaces(text: str) -> str:
"""Restore lost spaces in PDFs using pyenchant.
Replace words not in a dictionary with nearest suggestion, which
if often two words separated by a space.
>>> restore_lost_spaces('Excerpts sometimeslose their spaces.')
'Excerpts sometimes lose their spaces.'
"""
checker = SpellChecker("en_US")
log.debug(text)
checker.set_text(text)
for error in checker:
assert error.word is not None # for typing
log.debug(f"{error.word}, {error.suggest()}")
for suggestion in error.suggest():
# Suggestion must be same as original with spaces removed
if error.word.replace(" ", "") == suggestion.replace(" ", ""):
error.replace(suggestion)
break
return str(checker.get_text()) # str() for typing
def _get_group_n(regex: re.Pattern, text: str, number: int) -> str | None:
"""Match function -- for typing."""
match = regex.search(text)
return match.group(number) if match else None
def parse_args(argv: list) -> argparse.Namespace:
"""Process arguments."""
# https://docs.python.org/3/library/argparse.html
arg_parser = argparse.ArgumentParser(
description="""Format (emailed) GoodRead annotation for use with
extract_dictation.py in
https://github.com/reagle/thunderdell
"""
)
# positional arguments
arg_parser.add_argument("file_names", nargs="*", type=Path, metavar="FILE_NAMES")
# optional arguments
arg_parser.add_argument(
"-f",
"--first",
type=int,
default=0,
help=r"""first page in actual PDF pagination,
can also be specified as annotation within PDF: `first = \d+`""",
)
arg_parser.add_argument(
"-o",
"--output-to-file",
action="store_true",
default=False,
help="output to FILE-fixed.txt",
)
arg_parser.add_argument(
"-t",
"--trash",
action="store_true",
default=False,
help="trash file after prompt for running extract-dictation",
)
arg_parser.add_argument(
"-L",
"--log-to-file",
action="store_true",
default=False,
help="log to file %(prog)s.log",
)
arg_parser.add_argument(
"-V",
"--verbose",
action="count",
default=0,
help="Increase verbosity (specify multiple times for more)",
)
arg_parser.add_argument("--version", action="version", version="0.1")
args = arg_parser.parse_args(argv)
log_level = (log.CRITICAL) - (args.verbose * 10)
LOG_FORMAT = "%(levelname).4s %(funcName).10s:%(lineno)-4d| %(message)s"
if args.log_to_file:
log.basicConfig(
filename="extract-goodreader.log",
filemode="w",
level=log_level,
format=LOG_FORMAT,
)
else:
log.basicConfig(level=log_level, format=LOG_FORMAT)
return args
if __name__ == "__main__":
args = parse_args(sys.argv[1:])
log.critical("==================================")
log.critical(f"{args=}")
for file_name in args.file_names:
text: str = ""
if file_name.suffix == ".eml":
with file_name.open("rb") as fp:
msg = BytesParser(policy=policy.default).parse(fp)
for part in msg.walk():
log.debug(f"{part=}")
msg_content_type = part.get_content_subtype()
log.debug(f"{msg_content_type=}")
if msg_content_type == "plain":
log.debug(f"part is plain: {msg_content_type}")
charset = part.get_content_charset(failobj="utf-8")
content = part.get_payload(decode=True).decode(
charset, "replace"
)
text = content
log.debug(f"TEXT IS:\n ```{text}```")
else:
raise TypeError(
f"Can extract text because {msg_content_type=} is unknown."
)
else:
text = file_name.read_text()
new_text = process_text(args, text)
fixed_fn = file_name.with_stem(file_name.stem + "-fixed").with_suffix(".txt")
if args.output_to_file:
fixed_fn.write_text(new_text)
subprocess.run(["open", str(fixed_fn)])
user_input = input(
"\nWhen you are done in the text editor, should I invoke"
+ " `extract_dictation.py`?\n"
+ " 'y' for yes,\n"
+ " 'yp' to also include `-p` (publish to social media)\n: "
)
if user_input.startswith("y"):
args.publish = False
if user_input == "yp":
args.publish = True
mm_file_name = file_name.with_suffix(".mm")
edited_text = fixed_fn.read_text()
create_mm(args, edited_text, mm_file_name)
subprocess.call(["open", "-a", "Freeplane.app", mm_file_name])
if args.trash or input("\nTrash file? 'y' for yes,\n") == "y":
detrius = [
file_name.stem + ".eml",
file_name.stem + "-fixed.txt",
file_name.stem + ".mm",
]
send2trash(detrius)
else:
print(new_text)